NorahDesk – a small non-coding RNA (ncRNA) detection tool for RNA sequencing (RNA-Seq) data

NorahDeskNorahDesk reconstructs full-length putative ncRNA transcripts from short sequence reads by hybridizing contigs. It analyzes not only the distinct read distribution of true ncRNA classes in an unbiased way but also utilizes secondary structures as an independent confirmation source to reliably predict ncRNA from deep sequencing data.

Using publicly available mouse sequence data from brain, skeletal muscle, testis and ovary, NorahDesk was evaluated with an emphasis on the performance for microRNAs (miRNAs) and piwi-interacting small RNA (piRNA). This method was also compared with Dario and mirDeep2 and found to produce longer transcripts with higher read coverage. This feature makes it the first method particularly suitable for the prediction of both known and novel piRNAs.

NorahDesk and the mouse small ncRNA annotation file in BED format used in this study are available at

  • Ragan C, Mowry BJ, Bauer DC. (2012) Hybridization-based reconstruction of small non-coding RNA transcripts from deep sequencing data. Nucleic Acids Res [Epub ahead of print]. [article]
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